Calaveras River HCP Stockton East Water District Calaveras River Habitat Conservation Plan Prepared By: Stockton East Water District and FISHBIO August 2019 Calaveras River HCP Executive Summary Overview The Calaveras River Habitat Conservation Plan (CHCP) describes operational criteria to support the biological goals of maintaining a viable population of rainbow trout and Central Valley steelhead (Oncorhynchus mykiss) within the CHCP boundaries, as well as maintaining adequate habitat condition upstream of Bellota for fall-, late fall-, spring- or winter-run Chinook salmon (Oncorhynchus tshawytscha) that may opportunistically migrate into the conservation area. While the CHCP intends to provide conditions that would support Chinook salmon should they migrate into the conservation area, these salmon are not expected to maintain a viable population based both on pre-dam and current conditions. The Calaveras River’s ability to support anadromous fish populations (such as steelhead and the various runs of Chinook salmon) is limited by the impoundment and operational criteria of New Hogan Dam and Reservoir, originally constructed in 1930 to ease flooding concerns for the City of Stockton. The CHCP allows Stockton East Water District (SEWD or District) to comply with the Endangered Species Act (ESA), protecting and managing fishery resources and habitat while maintaining reliable water delivery to its constituents. The District is seeking a 50-year Incidental Take Permit (ITP) for ESA-listed species under the authority of the National Marine Fisheries Service (NMFS). Throughout the multi-year development of the CHCP, the District has worked closely with NMFS and other interested stakeholders as part of the Calaveras River Technical Review Group (including the U.S. Fish and Wildlife Service and California Department of Fish and Wildlife) to develop operational criteria that would help maintain the health of the Calaveras River fisheries resources. Over the term of the ITP, this working relationship is expected to continue with biannual review meetings between interested parties. Geographic Scope The Calaveras River is a small, regulated tributary to the San Joaquin River and serves as an important source of surface water for agricultural and municipal uses in Calaveras and San Joaquin counties. SEWD’s management of this precious resource on behalf of its constituents over the past forty years has created conditions which support a healthy rainbow trout fishery characterized by relatively high abundance and fish condition factors recorded during the various monitoring efforts conducted by SEWD biologists and by anecdotal accounts from local fishermen. The plan area boundary is limited to the lower Calaveras River and its adjacent riparian zone between New Hogan Dam and the confluence with the San Joaquin River, as well as the New Hogan Reservoir. The CHCP boundaries encompass those waterways that are potentially accessible to the Covered Species within the District’s service area, including: ● Lower Calaveras River from New Hogan Dam (RM 42) to the confluence where it enters the San Joaquin Delta (RM 0) via both the Old Calaveras River channel and Mormon Slough/Stockton Diverting Canal (SDC) routes. 2 Calaveras River HCP ● Potter Creek from the headwaters to its two branches (North and South) and its two confluences with Mormon Slough– North branch enters Mormon Slough at the old Southern Pacific Railroad Bridge and the South branch enters Mormon Slough just upstream of Panella Dam. ● Mosher Slough/Creek from the headwaters at Mosher Creek Dam to its confluence with Pixley Slough/Bear Creek. Covered Activities The primary goal of the CHCP is to obtain authorization for the take of ESA-listed species that may be affected by the District’s operations and maintenance activities within the boundaries of the defined area. The activities the District is seeking to be covered include: ● The impoundment and non-flood control operations of water from New Hogan Reservoir. ● The operation of the Old Calaveras River Headworks facility. ● The operation of the Bellota Diversion facility. ● The operation of small instream flashboard dams within the District’s service area. ● The operation and improvement of privately-owned diversion facilities within the District’s service area. ● Channel maintenance operations for instream structures within the District’s service area. ● District fisheries monitoring program. A small amount of annual take has been requested for fish that may incidentally occur and be affected by operations and/or maintenance activities on an annual basis, in addition to a supplementary fisheries monitoring program designed to assess salmonid populations throughout all phases of their life history. All activities will follow best management practices in order to minimize the effect of the activity on ESA-listed species. Covered Species As all activities are related to instream and/or water delivery operations, the District is seeking coverage for fish species that occur or may occur, in the case of winter- or spring-run Chinook salmon, or have critical habitat designated within the CHCP boundary. The California Central Valley (CCV) steelhead distinct population segment (DPS)1, which includes the Calaveras River, are currently listed as threatened (63 FR 13347; 65 FR 42422; 70 FR 37160) under the federal Endangered Species Act (ESA) by the National Marine Fisheries Service (NMFS). Multiple runs of Chinook salmon (fall-, late fall-, spring-, or winter-run) may opportunistically utilize the Calaveras River over the term of the ITP. The fall-run Chinook salmon is the evolutionarily significant unit (ESU)most frequently reported in the San Joaquin basin and, while not currently listed under the ESA, it is considered a Species of Concern (69 FR 19975) by 1 The ESA defines a “species” to include any distinct population segment of any species of vertebrate fish or wildlife. For Pacific salmon, NOAA Fisheries Service considers an evolutionarily significant unit, or “ESU,” a “species” under the ESA. For Pacific steelhead, NOAA has delineated distinct population segments (DPSs) for consideration as “species” under the ESA. 3 Calaveras River HCP NMFS and a Species of Special Concern by the California Department of Fish and Wildlife (CDFW). While the importance of the Calaveras River for steelhead production is currently unknown, the Calaveras River is classified as a Core 1 watershed, which means it has the potential to support a viable steelhead population. However, its utility as a salmon-supporting stream is highly limited. The District recognizes the potential problems for salmonids caused by its operations within the Mormon Slough flood control channel, Old Calaveras River channel, and its facilities. While the CHCP intends to provide conditions (improved fish passage, reduced entrainment, minimum instream flow, etc.) that would support Chinook salmon should they migrate into the project area, these salmon are not expected to maintain a viable population based both on pre-dam and current conditions. Conservation Strategies In general, conservation strategies have been designed to support the biological goals of the CHCP, which are to: ● maintain a viable population of O. mykiss within the conservation area ● maintain adequate habitat conditions upstream of Bellota for fall-, late-fall-, spring-, or winter-run Chinook salmon that may opportunistically migrate into the conservation area but are not expected to maintain a viable population based on both pre-dam and current conditions. These biological goals are divided into specific biological objectives that identify the various conservation measures needed to achieve the biological goals. Five biological objectives have been identified (i.e., Flow, Fish Passage, Avoid/Minimize Fish Entrainment, Water Quality, and Avoid/Minimize Direct Fish Injury/Mortality) and each includes metrics, referred to as targets, to track progress toward achieving the particular objective and goals. The District has developed a series of best management practices regarding the described operations and maintenance activities in order to best achieve the stated biological goals and meet the specified targets identified in the biological objectives. Adaptive Management and Monitoring The CHCP’s Adaptive Management Plan (AMP) provides guidance regarding the manner in which the monitoring information collected by the District, as well as information collected by others (e.g., USFWS and CDFW), will be used to continually evaluate and, if necessary, modify the CHCP implementation and long-term management of environmental resources. Collecting and analyzing data through monitoring and research are essential components of the AMP. Conservation strategies are expected to effectively achieve the plan’s biological goals, objectives, and associated targets since they were designed based on the best scientific information currently available. If effectiveness monitoring indicates that the desired results of the conservation strategies are not being achieved, or if other information needs to be incorporated into the CHCP, then adjustments in the conservation and mitigation strategies can be made to account for changing 4 Calaveras River HCP conditions and new scientific information. The District has committed to participating in biannual meetings in order to review data obtained and implement adaptive management activities, if needed. Since 2001, SEWD has voluntarily implemented several temporary and permanent fish passage